From the description, it's kind of difficult to tell what might be the matter. A comet and a "common" are the same kind of goldfish. Were these two feeders? If this is the case, sometimes the rough handling conditions and breeding can lead to problems that don't appear until the fish gets older. I hate to say so, but sometimes genetics can be a factor in goldfish. You just don't know what happened. You don't say how big these fish are, but at over a year, a comet can easily grow to 6 to 8 inches. In a 45 gallon, that can be a little tight with two of them. Have they always been in a 45, or were they in a smaller tank when younger. Is it possible that the affected fish has experienced some kind of stunting?
You say there are no white spots, but are there any signs of streaking? Damage to the fins? Are the fins of the affected fish clamped? Just looking for a clue that might help you to solve the mystery.